This SBIR Phase I project proposes to develop a novel technology platform for very high throughput multiplexing important for genotyping and pathogen detection. A unique barcoding scheme for bead-based assays with the potential of individually labeling millions of samples is combined with a high speed laser scanning instrument developed by Blueshift Biotechnologies, Inc. (BBI). The proposed scanning system will combine two lasers: one for interrogating fluorophore labeled oligonucleotides, and the other for measuring bead encoding. The robust and cost-effective design will enable fast readout of very highly multiplexed samples and provide a workable platform for highly multiplexed genotyping applications. The system also will employ a novel anisotropy measurement scheme to provide superior discrimination of incorporated from free fluorophore. This powerful technique enables high throughput genotyping, such as the typing of microbial and viral pathogens by sequence detection in homogeneous assay formats. The combination of fast sequence signature detection in homogeneous assays will provide a powerful commercial platform for pharmacogenomics, biodefense, diagnostics, and other medically important applications. The optical encoding system is based on rare earth upconverting phosphor (RUP) materials. The unique optical properties of RUPs enable high throughput particle multiplexing, identifying >105 times more samples than the best current optical barcoding scheme. The use of multiplexing based on the ratios of more than one RUP within a single particle has been developed by Parallel Synthesis Technologies, Inc. (PSTI). They have demonstrated that it is possible to resolve >300 individual ratios from a two-color RUP system. It is estimated that about 3 x 10/7 and 6 x 10/9 uniquely labeled samples are possible with a four- or five-color RUP system, respectively.